diff --git a/src-tauri/src/commands/config.rs b/src-tauri/src/commands/config.rs
index 0fa6e4a20..60c0f1c79 100644
--- a/src-tauri/src/commands/config.rs
+++ b/src-tauri/src/commands/config.rs
@@ -212,20 +212,22 @@ pub async fn set_claude_common_config_snippet(
     snippet: String,
     state: tauri::State<'_, crate::store::AppState>,
 ) -> Result<(), String> {
+    let is_cleared = snippet.trim().is_empty();
+
     if !snippet.trim().is_empty() {
         serde_json::from_str::<serde_json::Value>(&snippet).map_err(invalid_json_format_error)?;
     }
 
-    let value = if snippet.trim().is_empty() {
-        None
-    } else {
-        Some(snippet)
-    };
+    let value = if is_cleared { None } else { Some(snippet) };
 
     state
         .db
         .set_config_snippet("claude", value)
         .map_err(|e| e.to_string())?;
+    state
+        .db
+        .set_config_snippet_cleared("claude", is_cleared)
+        .map_err(|e| e.to_string())?;
     Ok(())
 }
 
@@ -246,6 +248,7 @@ pub async fn set_common_config_snippet(
     snippet: String,
     state: tauri::State<'_, crate::store::AppState>,
 ) -> Result<(), String> {
+    let is_cleared = snippet.trim().is_empty();
     let old_snippet = state
         .db
         .get_config_snippet(&app_type)
@@ -253,11 +256,7 @@ pub async fn set_common_config_snippet(
 
     validate_common_config_snippet(&app_type, &snippet)?;
 
-    let value = if snippet.trim().is_empty() {
-        None
-    } else {
-        Some(snippet)
-    };
+    let value = if is_cleared { None } else { Some(snippet) };
 
     if matches!(app_type.as_str(), "claude" | "codex" | "gemini") {
         if let Some(legacy_snippet) = old_snippet
@@ -278,6 +277,10 @@ pub async fn set_common_config_snippet(
         .db
         .set_config_snippet(&app_type, value)
         .map_err(|e| e.to_string())?;
+    state
+        .db
+        .set_config_snippet_cleared(&app_type, is_cleared)
+        .map_err(|e| e.to_string())?;
 
     if matches!(app_type.as_str(), "claude" | "codex" | "gemini") {
         let app = AppType::from_str(&app_type).map_err(|e| e.to_string())?;
diff --git a/src-tauri/src/commands/provider.rs b/src-tauri/src/commands/provider.rs
index c9f2b6ea3..344b35ecc 100644
--- a/src-tauri/src/commands/provider.rs
+++ b/src-tauri/src/commands/provider.rs
@@ -103,16 +103,16 @@ fn import_default_config_internal(state: &AppState, app_type: AppType) -> Result
         // Extract common config snippet (mirrors old startup logic in lib.rs)
         if state
             .db
-            .get_config_snippet(app_type.as_str())
-            .ok()
-            .flatten()
-            .is_none()
+            .should_auto_extract_config_snippet(app_type.as_str())?
         {
             match ProviderService::extract_common_config_snippet(state, app_type.clone()) {
                 Ok(snippet) if !snippet.is_empty() && snippet != "{}" => {
                     let _ = state
                         .db
                         .set_config_snippet(app_type.as_str(), Some(snippet));
+                    let _ = state
+                        .db
+                        .set_config_snippet_cleared(app_type.as_str(), false);
                 }
                 _ => {}
             }
diff --git a/src-tauri/src/database/dao/settings.rs b/src-tauri/src/database/dao/settings.rs
index 6f15b2585..bca48bcbf 100644
--- a/src-tauri/src/database/dao/settings.rs
+++ b/src-tauri/src/database/dao/settings.rs
@@ -7,6 +7,12 @@ use crate::error::AppError;
 use rusqlite::params;
 
 impl Database {
+    const LEGACY_COMMON_CONFIG_MIGRATED_KEY: &'static str = "common_config_legacy_migrated_v1";
+
+    fn config_snippet_cleared_key(app_type: &str) -> String {
+        format!("common_config_{app_type}_cleared")
+    }
+
     /// 获取设置值
     pub fn get_setting(&self, key: &str) -> Result<Option<String>, AppError> {
         let conn = lock_conn!(self.conn);
@@ -45,6 +51,60 @@ impl Database {
         self.get_setting(&format!("common_config_{app_type}"))
     }
 
+    /// 检查通用配置片段是否被用户显式清空
+    pub fn is_config_snippet_cleared(&self, app_type: &str) -> Result<bool, AppError> {
+        Ok(self
+            .get_setting(&Self::config_snippet_cleared_key(app_type))?
+            .as_deref()
+            == Some("true"))
+    }
+
+    /// 设置通用配置片段是否被显式清空
+    pub fn set_config_snippet_cleared(
+        &self,
+        app_type: &str,
+        cleared: bool,
+    ) -> Result<(), AppError> {
+        let key = Self::config_snippet_cleared_key(app_type);
+        if cleared {
+            self.set_setting(&key, "true")
+        } else {
+            let conn = lock_conn!(self.conn);
+            conn.execute("DELETE FROM settings WHERE key = ?1", params![key])
+                .map_err(|e| AppError::Database(e.to_string()))?;
+            Ok(())
+        }
+    }
+
+    /// 当前是否允许从 live 配置自动抽取通用配置片段
+    pub fn should_auto_extract_config_snippet(&self, app_type: &str) -> Result<bool, AppError> {
+        Ok(self.get_config_snippet(app_type)?.is_none()
+            && !self.is_config_snippet_cleared(app_type)?)
+    }
+
+    /// 检查历史通用配置迁移是否已经执行过
+    pub fn is_legacy_common_config_migrated(&self) -> Result<bool, AppError> {
+        Ok(self
+            .get_setting(Self::LEGACY_COMMON_CONFIG_MIGRATED_KEY)?
+            .as_deref()
+            == Some("true"))
+    }
+
+    /// 标记历史通用配置迁移已经执行完成
+    pub fn set_legacy_common_config_migrated(&self, migrated: bool) -> Result<(), AppError> {
+        if migrated {
+            self.set_setting(Self::LEGACY_COMMON_CONFIG_MIGRATED_KEY, "true")
+        } else {
+            let conn = lock_conn!(self.conn);
+            conn.execute(
+                "DELETE FROM settings WHERE key = ?1",
+                params![Self::LEGACY_COMMON_CONFIG_MIGRATED_KEY],
+            )
+            .map_err(|e| AppError::Database(e.to_string()))?;
+            Ok(())
+        }
+    }
+
     /// 设置通用配置片段
     pub fn set_config_snippet(
         &self,
diff --git a/src-tauri/src/lib.rs b/src-tauri/src/lib.rs
index 16550f49b..edbd8727e 100644
--- a/src-tauri/src/lib.rs
+++ b/src-tauri/src/lib.rs
@@ -560,78 +560,6 @@ pub fn run() {
                 }
             }
 
-            // 5. Auto-extract common config snippets from live files (when snippet is missing)
-            for app_type in crate::app_config::AppType::all() {
-                // Skip if snippet already exists
-                if app_state
-                    .db
-                    .get_config_snippet(app_type.as_str())
-                    .ok()
-                    .flatten()
-                    .is_some()
-                {
-                    continue;
-                }
-
-                // Try to read the live config file for this app type
-                let settings =
-                    match crate::services::provider::ProviderService::read_live_settings(
-                        app_type.clone(),
-                    ) {
-                        Ok(s) => s,
-                        Err(_) => continue, // No live config file, skip silently
-                    };
-
-                // Extract common config (strip provider-specific fields)
-                match crate::services::provider::ProviderService::extract_common_config_snippet_from_settings(
-                    app_type.clone(),
-                    &settings,
-                ) {
-                    Ok(snippet) if !snippet.is_empty() && snippet != "{}" => {
-                        match app_state
-                            .db
-                            .set_config_snippet(app_type.as_str(), Some(snippet))
-                        {
-                            Ok(()) => log::info!(
-                                "✓ Auto-extracted common config snippet for {}",
-                                app_type.as_str()
-                            ),
-                            Err(e) => log::warn!(
-                                "✗ Failed to save config snippet for {}: {e}",
-                                app_type.as_str()
-                            ),
-                        }
-                    }
-                    Ok(_) => log::debug!(
-                        "○ Live config for {} has no extractable common fields",
-                        app_type.as_str()
-                    ),
-                    Err(e) => log::warn!(
-                        "✗ Failed to extract config snippet for {}: {e}",
-                        app_type.as_str()
-                    ),
-                }
-            }
-
-            // 5.1 Migrate legacy providers that relied on inferred common-config usage
-            for app_type in [
-                crate::app_config::AppType::Claude,
-                crate::app_config::AppType::Codex,
-                crate::app_config::AppType::Gemini,
-            ] {
-                if let Err(e) =
-                    crate::services::provider::ProviderService::migrate_legacy_common_config_usage_if_needed(
-                        &app_state,
-                        app_type.clone(),
-                    )
-                {
-                    log::warn!(
-                        "✗ Failed to migrate legacy common-config usage for {}: {e}",
-                        app_type.as_str()
-                    );
-                }
-            }
-
             // 迁移旧的 app_config_dir 配置到 Store
             if let Err(e) = app_store::migrate_app_config_dir_from_settings(app.handle()) {
                 log::warn!("迁移 app_config_dir 失败: {e}");
@@ -816,6 +744,8 @@ pub fn run() {
                     }
                 }
 
+                initialize_common_config_snippets(&state);
+
                 // 检查 settings 表中的代理状态，自动恢复代理服务
                 restore_proxy_state_on_startup(&state).await;
 
@@ -1324,6 +1254,85 @@ async fn restore_proxy_state_on_startup(state: &store::AppState) {
     }
 }
 
+fn initialize_common_config_snippets(state: &store::AppState) {
+    // Auto-extract common config snippets from clean live files when snippet is missing.
+    // This must run before proxy takeover is restored on startup, otherwise we'd read
+    // proxy-placeholder configs instead of the user's actual live settings.
+    for app_type in crate::app_config::AppType::all() {
+        if !state
+            .db
+            .should_auto_extract_config_snippet(app_type.as_str())
+            .unwrap_or(false)
+        {
+            continue;
+        }
+
+        let settings = match crate::services::provider::ProviderService::read_live_settings(
+            app_type.clone(),
+        ) {
+            Ok(s) => s,
+            Err(_) => continue,
+        };
+
+        match crate::services::provider::ProviderService::extract_common_config_snippet_from_settings(
+            app_type.clone(),
+            &settings,
+        ) {
+            Ok(snippet) if !snippet.is_empty() && snippet != "{}" => {
+                match state.db.set_config_snippet(app_type.as_str(), Some(snippet)) {
+                    Ok(()) => {
+                        let _ = state.db.set_config_snippet_cleared(app_type.as_str(), false);
+                        log::info!(
+                            "✓ Auto-extracted common config snippet for {}",
+                            app_type.as_str()
+                        );
+                    }
+                    Err(e) => log::warn!(
+                        "✗ Failed to save config snippet for {}: {e}",
+                        app_type.as_str()
+                    ),
+                }
+            }
+            Ok(_) => log::debug!(
+                "○ Live config for {} has no extractable common fields",
+                app_type.as_str()
+            ),
+            Err(e) => log::warn!(
+                "✗ Failed to extract config snippet for {}: {e}",
+                app_type.as_str()
+            ),
+        }
+    }
+
+    let should_run_legacy_migration = state
+        .db
+        .is_legacy_common_config_migrated()
+        .map(|done| !done)
+        .unwrap_or(true);
+
+    if should_run_legacy_migration {
+        for app_type in [
+            crate::app_config::AppType::Claude,
+            crate::app_config::AppType::Codex,
+            crate::app_config::AppType::Gemini,
+        ] {
+            if let Err(e) = crate::services::provider::ProviderService::migrate_legacy_common_config_usage_if_needed(
+                state,
+                app_type.clone(),
+            ) {
+                log::warn!(
+                    "✗ Failed to migrate legacy common-config usage for {}: {e}",
+                    app_type.as_str()
+                );
+            }
+        }
+
+        if let Err(e) = state.db.set_legacy_common_config_migrated(true) {
+            log::warn!("✗ Failed to persist legacy common-config migration flag: {e}");
+        }
+    }
+}
+
 // ============================================================
 // 迁移错误对话框辅助函数
 // ============================================================
diff --git a/src-tauri/src/services/provider/mod.rs b/src-tauri/src/services/provider/mod.rs
index 508c2a8d4..bbae722ca 100644
--- a/src-tauri/src/services/provider/mod.rs
+++ b/src-tauri/src/services/provider/mod.rs
@@ -614,6 +614,46 @@ impl ProviderService {
         state: &AppState,
         app_type: AppType,
     ) -> Result<(), AppError> {
+        if app_type.is_additive_mode() {
+            return sync_current_provider_for_app_to_live(state, &app_type);
+        }
+
+        let current_id =
+            match crate::settings::get_effective_current_provider(&state.db, &app_type)? {
+                Some(id) => id,
+                None => return Ok(()),
+            };
+
+        let providers = state.db.get_all_providers(app_type.as_str())?;
+        let Some(provider) = providers.get(&current_id) else {
+            return Ok(());
+        };
+
+        let takeover_enabled =
+            futures::executor::block_on(state.db.get_proxy_config_for_app(app_type.as_str()))
+                .map(|config| config.enabled)
+                .unwrap_or(false);
+
+        let has_live_backup =
+            futures::executor::block_on(state.db.get_live_backup(app_type.as_str()))
+                .ok()
+                .flatten()
+                .is_some();
+
+        let live_taken_over = state
+            .proxy_service
+            .detect_takeover_in_live_config_for_app(&app_type);
+
+        if takeover_enabled && (has_live_backup || live_taken_over) {
+            futures::executor::block_on(
+                state
+                    .proxy_service
+                    .update_live_backup_from_provider(app_type.as_str(), provider),
+            )
+            .map_err(|e| AppError::Message(format!("更新 Live 备份失败: {e}")))?;
+            return Ok(());
+        }
+
         sync_current_provider_for_app_to_live(state, &app_type)
     }
 
diff --git a/src-tauri/tests/provider_service.rs b/src-tauri/tests/provider_service.rs
index 903d86dfa..c4400c230 100644
--- a/src-tauri/tests/provider_service.rs
+++ b/src-tauri/tests/provider_service.rs
@@ -238,6 +238,184 @@ command = "say"
     );
 }
 
+#[test]
+fn sync_current_provider_for_app_keeps_live_takeover_and_updates_restore_backup() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    let _home = ensure_test_home();
+
+    let mut config = MultiAppConfig::default();
+    {
+        let manager = config
+            .get_manager_mut(&AppType::Claude)
+            .expect("claude manager");
+        manager.current = "current-provider".to_string();
+
+        let mut provider = Provider::with_id(
+            "current-provider".to_string(),
+            "Current".to_string(),
+            json!({
+                "env": {
+                    "ANTHROPIC_AUTH_TOKEN": "real-token",
+                    "ANTHROPIC_BASE_URL": "https://claude.example"
+                }
+            }),
+            None,
+        );
+        provider.meta = Some(ProviderMeta {
+            common_config_enabled: Some(true),
+            ..Default::default()
+        });
+
+        manager
+            .providers
+            .insert("current-provider".to_string(), provider);
+    }
+
+    let state = create_test_state_with_config(&config).expect("create test state");
+    state
+        .db
+        .set_config_snippet(
+            AppType::Claude.as_str(),
+            Some(r#"{ "includeCoAuthoredBy": false }"#.to_string()),
+        )
+        .expect("set common config snippet");
+
+    let taken_over_live = json!({
+        "env": {
+            "ANTHROPIC_BASE_URL": "http://127.0.0.1:5000",
+            "ANTHROPIC_AUTH_TOKEN": "PROXY_MANAGED"
+        }
+    });
+    let settings_path = get_claude_settings_path();
+    std::fs::create_dir_all(settings_path.parent().expect("settings dir")).expect("create dir");
+    std::fs::write(
+        &settings_path,
+        serde_json::to_string_pretty(&taken_over_live).expect("serialize taken over live"),
+    )
+    .expect("write taken over live");
+
+    futures::executor::block_on(state.db.save_live_backup("claude", "{\"env\":{}}"))
+        .expect("seed live backup");
+
+    let mut proxy_config = futures::executor::block_on(state.db.get_proxy_config_for_app("claude"))
+        .expect("get proxy config");
+    proxy_config.enabled = true;
+    futures::executor::block_on(state.db.update_proxy_config_for_app(proxy_config))
+        .expect("enable takeover");
+
+    ProviderService::sync_current_provider_for_app(&state, AppType::Claude)
+        .expect("sync current provider should succeed");
+
+    let live_after: serde_json::Value =
+        read_json_file(&settings_path).expect("read live settings after sync");
+    assert_eq!(
+        live_after, taken_over_live,
+        "sync should not overwrite live config while takeover is active"
+    );
+
+    let backup = futures::executor::block_on(state.db.get_live_backup("claude"))
+        .expect("get live backup")
+        .expect("backup exists");
+    let backup_value: serde_json::Value =
+        serde_json::from_str(&backup.original_config).expect("parse backup value");
+
+    assert_eq!(
+        backup_value
+            .get("includeCoAuthoredBy")
+            .and_then(|v| v.as_bool()),
+        Some(false),
+        "restore backup should receive the updated effective config"
+    );
+    assert_eq!(
+        backup_value
+            .get("env")
+            .and_then(|v| v.get("ANTHROPIC_AUTH_TOKEN"))
+            .and_then(|v| v.as_str()),
+        Some("real-token"),
+        "restore backup should preserve the provider token rather than proxy placeholder"
+    );
+}
+
+#[test]
+fn explicitly_cleared_common_snippet_is_not_auto_extracted() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    let _home = ensure_test_home();
+
+    let state = create_test_state().expect("create test state");
+    state
+        .db
+        .set_config_snippet_cleared(AppType::Claude.as_str(), true)
+        .expect("mark snippet explicitly cleared");
+
+    assert!(
+        !state
+            .db
+            .should_auto_extract_config_snippet(AppType::Claude.as_str())
+            .expect("check auto-extract eligibility"),
+        "explicitly cleared snippets should block auto-extraction"
+    );
+
+    state
+        .db
+        .set_config_snippet(AppType::Claude.as_str(), Some("{}".to_string()))
+        .expect("set snippet");
+    state
+        .db
+        .set_config_snippet_cleared(AppType::Claude.as_str(), false)
+        .expect("clear explicit-empty marker");
+
+    assert!(
+        !state
+            .db
+            .should_auto_extract_config_snippet(AppType::Claude.as_str())
+            .expect("check auto-extract after snippet saved"),
+        "existing snippets should also block auto-extraction"
+    );
+}
+
+#[test]
+fn legacy_common_config_migration_flag_roundtrip() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    let _home = ensure_test_home();
+
+    let state = create_test_state().expect("create test state");
+
+    assert!(
+        !state
+            .db
+            .is_legacy_common_config_migrated()
+            .expect("initial migration flag"),
+        "migration flag should default to false"
+    );
+
+    state
+        .db
+        .set_legacy_common_config_migrated(true)
+        .expect("set migration flag");
+    assert!(
+        state
+            .db
+            .is_legacy_common_config_migrated()
+            .expect("read migration flag"),
+        "migration flag should persist once set"
+    );
+
+    state
+        .db
+        .set_legacy_common_config_migrated(false)
+        .expect("clear migration flag");
+    assert!(
+        !state
+            .db
+            .is_legacy_common_config_migrated()
+            .expect("read migration flag after clear"),
+        "migration flag should be removable for tests/debugging"
+    );
+}
+
 #[test]
 fn switch_packycode_gemini_updates_security_selected_type() {
     let _guard = test_mutex().lock().expect("acquire test mutex");